The slim line jewel cases are going to be a problem. Storage systems for CDs and DVDs are designed to accomodate the full size jewel cases. If space is at a premium (and it sounds like it is) you can use the jewel cases that store 2 disks in a singe jewel case. I use them whenever I can.
I also use the cheap Fellowes modular jewel case storage units, so I can add more whenever I need to. But they definately would not pass for furniture, and they can take up a lot of wall space if you're planning to store 200+ disks. They can hold 30 standard jewel cases, plus 3 of the 4-disk jewel cases (if you can still find them). They're 7" high, 18" wide and 5" deep. (You could lie them down and slide them under the beds, I suppose.)